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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ), 'gf_id' => 'HOM05D001528', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001528' ), 'data_identifier' => 'HOM05D001528', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001528', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '416', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p21480' => 'bna', 'A10p17640' => 'bna', 'Aa31LG1G12460' => 'aar', 'Aa31LG4G14610' => 'aar', 'Aa31LG5G7750' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2142' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4081' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4591' => 'aag', 'Actinidia03036' => 'ach', 'Actinidia07004' => 'ach', 'Actinidia24085' => 'ach', 'Actinidia24484' => 'ach', 'Ah.01g002770' => 'amhyb', 'Ah.01g015040' => 'amhyb', 'Ah.16g108440' => 'amhyb', 'AL5G23900' => 'aly', 'AL5G23910' => 'aly', 'AL8G37030' => 'aly', 'Aqoxy4G03226' => 'aox', 'Aqoxy4G03235' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3T264X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66AXQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.792I4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7W6G1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AP35ED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C0Z8UU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FH9TUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3ZIFI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RQ1X88' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X2FBQZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX95HC' => 'arhy', 'AT3G45300' => 'ath', 'AT5G60410' => 'ath', 'ATR0314G031' => 'atr', 'ATR0314G036' => 'atr', 'Atru.chr12.708' => 'acertr', 'Atru.chr12.719' => 'acertr', 'Atru.chr3.3674' => 'acertr', 'Atru.chr3.3676' => 'acertr', 'Atru.chr3.3682' => 'acertr', 'AUR62006526' => 'cqu', 'AUR62006528' => 'cqu', 'AUR62020764' => 'cqu', 'AUR62025007' => 'cqu', 'AUR62025010' => 'cqu', 'AUR62027948' => 'cqu', 'BcaB01g01091' => 'bca', 'BcaB01g01092' => 'bca', 'BcaB05g22639' => 'bca', 'BcaB08g36340' => 'bca', 'BcaC01g01974' => 'bca', 'BcaC01g01975' => 'bca', 'BcaC03g13975' => 'bca', 'BcaC04g19701' => 'bca', 'BolC2t07268H' => 'bol', 'BolC3t19251H' => 'bol', 'BolC9t58178H' => 'bol', 'BraA02t05729Z' => 'bra', 'BraA06t25231Z' => 'bra', 'BraA06t25232Z' => 'bra', 'BraA10t43843Z' => 'bra', 'C02p11710' => 'bna', 'C03p69900' => 'bna', 'C09p53040' => 'bna', 'CAN.G591.1' => 'can', 'CAN.G631.3' => 'can', 'CAN.G631.6' => 'can', 'CAN.G65.194' => 'can', 'CANSAT54G0167' => 'cansat', 'CANSAT54G0682' => 'cansat', 'CARHR118250' => 'chi', 'CARHR150570' => 'chi', 'CARHR150580' => 'chi', 'CARHR150590' => 'chi', 'CARHR274090' => 'chi', 'Carub.0005s1117' => 'cru', 'Carub.0005s1118' => 'cru', 'Carub.0008s2112' => 'cru', 'Ca_01430_v3' => 'car', 'Ca_19246_v3' => 'car', 'Ca_19248_v3' => 'car', 'CBR_g4437' => 'cbr', 'Cc01_g11420' => 'ccan', 'Cc01_g11440' => 'ccan', 'CDE04G1160' => 'cde', 'CDE07G0821' => 'cde', 'CDE09G0084' => 'cde', 'CDE09G0354' => 'cde', 'Cfa022808' => 'cfa', 'Cfa023184' => 'cfa', 'Cfa025513' => 'cfa', 'Cfa026122' => 'cfa', 'Cfa027299' => 'cfa', 'Ciclev10028544m.g' => 'ccl', 'Ciclev10030028m.g' => 'ccl', 'Ciclev10031116m.g' => 'ccl', 'CiPaw.01G275100' => 'cil', 'CiPaw.13G108100' => 'cil', 'CiPaw.13G108200' => 'cil', 'CiPaw.14G078300' => 'cil', 'ClCG02G021020' => 'cla', 'ClCG03G002320' => 'cla', 'COL.COLO4_05185' => 'col', 'COL.COLO4_05188' => 'col', 'COL.COLO4_05189' => 'col', 'COL.COLO4_05190' => 'col', 'COL.COLO4_23720' => 'col', 'Cpa.g.sc139.76' => 'cpa', 'Cpa.g.sc139.79' => 'cpa', 'Cre06.g296400' => 'cre', 'Cre12.g500900' => 'cre', 'CsaV3_1G013000' => 'csa', 'CsaV3_1G030150' => 'csa', 'CsaV3_6G021710' => 'csa', 'CSS0002841' => 'camsi', 'CSS0006864' => 'camsi', 'CSS0039044' => 'camsi', 'CSS0044348' => 'camsi', 'CSS0044970' => 'camsi', 'DCAR_005474' => 'dca', 'DCAR_015556' => 'dca', 'DCAR_018828' => 'dca', 'DCAR_019131' => 'dca', 'DCAR_026639' => 'dca', 'Dinv06399' => 'din', 'Dinv24621' => 'din', 'Dinv32775' => 'din', 'Dinv32778' => 'din', 'Dinv35726' => 'din', 'Duzib106G0190' => 'dzi', 'Duzib150G0353' => 'dzi', 'Duzib168G0357' => 'dzi', 'Duzib168G1679' => 'dzi', 'ECA233G3194' => 'eca', 'ECA233G6159' => 'eca', 'ECA240G4237' => 'eca', 'ECA248G0966' => 'eca', 'EL10Ac2g03583' => 'bvu', 'EL10Ac9g22476' => 'bvu', 'EL10Ac9g22477' => 'bvu', 'EL10Ac9g22484' => 'bvu', 'EL10As4g23420' => 'bvu', 'Eucgr.B02470' => 'egr', 'Eucgr.B02476' => 'egr', 'Eucgr.B02478' => 'egr', 'Eucgr.B02479' => 'egr', 'FAN01G0801' => 'fan', 'FAN01G1814' => 'fan', 'FAN03G0078' => 'fan', 'FAN06G3342' => 'fan', 'FAN10G2321' => 'fan', 'FAN11G1754' => 'fan', 'FAN11G2701' => 'fan', 'FAN16G3551' => 'fan', 'FAN21G0986' => 'fan', 'FAN21G1847' => 'fan', 'FAN25G2184' => 'fan', 'FAN25G2987' => 'fan', 'FvH4_3g32900' => 'fve', 'FvH4_3g32990' => 'fve', 'FvH4_7g19970' => 'fve', 'Glyma.11G154005' => 'gma', 'Glyma.11G154423' => 'gma', 'Glyma.12G071100' => 'gma', 'Glyma.12G071300' => 'gma', 'Glyma.12G170900' => 'gma', 'Glyma.13G328100' => 'gma', 'Gohir.A09G106300' => 'ghi', 'Gohir.A13G220800' => 'ghi', 'Gohir.A13G220900' => 'ghi', 'Gohir.D09G103000' => 'ghi', 'Gohir.D13G224800' => 'ghi', 'Gohir.D13G224850' => 'ghi', 'Gohir.D13G224900' => 'ghi', 'Gorai.006G120500' => 'gra', 'Gorai.013G255600' => 'gra', 'Gorai.013G255700' => 'gra', 'GSVIVG01025151001' => 'vvi', 'GSVIVG01025158001' => 'vvi', 'HanXRQChr01g0018241' => 'han', 'HanXRQChr02g0055901' => 'han', 'HanXRQChr07g0197391' => 'han', 'HanXRQChr07g0197401' => 'han', 'HanXRQChr08g0219601' => 'han', 'HanXRQChr10g0291121' => 'han', 'HanXRQChr13g0404431' => 'han', 'HanXRQChr14g0453001' => 'han', 'Haze_16923' => 'cav', 'Haze_23896' => 'cav', 'Haze_23898' => 'cav', 'Haze_26447' => 'cav', 'Haze_27126' => 'cav', 'Hma1.2p1_0071F.1_g038120' => 'hma', 'Hma1.2p1_0071F.1_g038170' => 'hma', 'Hma1.2p1_0568F.1_g180120' => 'hma', 'Hma1.2p1_2977F.1_g331190' => 'hma', 'HPP92_001045' => 'vpl', 'HPP92_003608' => 'vpl', 'HPP92_003609' => 'vpl', 'HPP92_019465' => 'vpl', 'HPP92_019466' => 'vpl', 'Hund01406' => 'sun', 'Hund08381' => 'sun', 'Hund22504' => 'sun', 'Lalb_Chr01g0004201' => 'lal', 'Lalb_Chr03g0027171' => 'lal', 'Lalb_Chr03g0027181' => 'lal', 'Lalb_Chr19g0137371' => 'lal', 'Lalb_Chr19g0137381' => 'lal', 'Lalb_Chr22g0350201' => 'lal', 'Lalb_Chr24g0394471' => 'lal', 'Lj1A187G24' => 'lonja', 'Lj1C186T6' => 'lonja', 'Lj2C1033G3' => 'lonja', 'Lj3g0004090' => 'lja', 'Lj3g0008308' => 'lja', 'Lj3g0021237' => 'lja', 'Lsat_1_v5_gn_1_65981' => 'lsa', 'Lsat_1_v5_gn_2_97920' => 'lsa', 'Lsat_1_v5_gn_2_97980' => 'lsa', 'Lsat_1_v5_gn_5_98140' => 'lsa', 'Lsat_1_v5_gn_6_46320' => 'lsa', 'Lsat_1_v5_gn_8_166521' => 'lsa', 'Lsat_1_v5_gn_8_20081' => 'lsa', 'Manes.04G024600' => 'mes', 'Manes.11G142100' => 'mes', 'Manes.11G142200' => 'mes', 'Mapoly0060s0062' => 'mpo', 'Mapoly0079s0031' => 'mpo', 'Mapoly0154s0036' => 'mpo', 'MBI05_g11572_MAGBIO' => 'mbi', 'MBI05_g31460_MAGBIO' => 'mbi', 'MBI05_g31462_MAGBIO' => 'mbi', 'MBI05_g31463_MAGBIO' => 'mbi', 'MBI15_g19419_MAGBIO' => 'mbi', 'MCO09G491' => 'mco', 'MCO11G020' => 'mco', 'MCO16G633' => 'mco', 'MD01G1111200' => 'mdo', 'MD03G1112700' => 'mdo', 'MD03G1116100' => 'mdo', 'MD07G1177400' => 'mdo', 'MD11G1131700' => 'mdo', 'Medtr0837s0010' => 'mtr', 'Medtr2057s0010' => 'mtr', 'Medtr2152s0010' => 'mtr', 'Medtr2g093730' => 'mtr', 'Medtr4g060480' => 'mtr', 'Medtr4g060510' => 'mtr', 'MELO3C005035.2' => 'cme', 'MELO3C025757.2' => 'cme', 'Migut.D02194' => 'egut', 'Migut.G00948' => 'egut', 'Migut.N02613' => 'egut', 'Migut.N02614' => 'egut', 'MSTRG.12325' => 'ama', 'MSTRG.18646' => 'ama', 'MSTRG.18648' => 'ama', 'Nitab4.5_0000471g0060' => 'nta', 'Nitab4.5_0000650g0010' => 'nta', 'Nitab4.5_0000999g0090' => 'nta', 'Nitab4.5_0000999g0110' => 'nta', 'Nitab4.5_0001275g0030' => 'nta', 'Nitab4.5_0001830g0030' => 'nta', 'Nitab4.5_0002186g0050' => 'nta', 'Nitab4.5_0002368g0160' => 'nta', 'Nitab4.5_0010831g0010' => 'nta', 'Nn2g10697' => 'nnu', 'Nn2g10717' => 'nnu', 'Nn2g13025' => 'nnu', 'Oeu002457.1' => 'oeu', 'Oeu019049.1' => 'oeu', 'Oeu035058.1' => 'oeu', 'Oeu044858.1' => 'oeu', 'Oeu059100.1' => 'oeu', 'Os01g0552850' => 'osa', 'Os03g0719100' => 'osa', 'Os05g0125000' => 'osa', 'Os05g0125500' => 'osa', 'Peaxi162Scf00351g00225' => 'pax', 'Peaxi162Scf00351g00327' => 'pax', 'Peaxi162Scf00973g00317' => 'pax', 'PGR102G2718' => 'pgr', 'PGR119G1340' => 'pgr', 'PGSC0003DMG400008113' => 'stu', 'PGSC0003DMG400008114' => 'stu', 'PGSC0003DMG400026901' => 'stu', 'Phvul.005G137000' => 'pvu', 'Phvul.011G073200' => 'pvu', 'Phvul.011G073500' => 'pvu', 'Potri.004G210200' => 'ptr', 'Potri.008G042300' => 'ptr', 'Potri.009G011700' => 'ptr', 'Potri.009G015000' => 'ptr', 'Potri.010G219600' => 'ptr', 'Pp3c16_2020' => 'ppa', 'Pp3c20_14150' => 'ppa', 'Pp3c20_14153' => 'ppa', 'Pp3c23_6780' => 'ppa', 'Pp3c24_13070' => 'ppa', 'Pp3c3_14940' => 'ppa', 'Pp3c8_11400' => 'ppa', 'PRCOL_00001565' => 'pco', 'PRCOL_00001797' => 'pco', 'PRCOL_00002017' => 'pco', 'PRCOL_00005382' => 'pco', 'PRCOL_00006254' => 'pco', 'PRCOL_00006365' => 'pco', 'PRCOL_00007230' => 'pco', 'Prupe.2G216700' => 'ppe', 'Prupe.6G097000' => 'ppe', 'Prupe.6G097600' => 'ppe', 'Psat5g277360' => 'psa', 'Psat7g223360' => 'psa', 'Psat7g223480' => 'psa', 'PSO017G7096' => 'pso', 'PSO339G0423' => 'pso', 'PSO339G4033' => 'pso', 'PSO339G5049' => 'pso', 'PSO349G0173' => 'pso', 'PSO384G1162' => 'pso', 'PSO384G1932' => 'pso', 'PSO478G0387' => 'pso', 'PSO591G0185' => 'pso', 'QL01p023217' => 'qlo', 'QL01p023251' => 'qlo', 'QL08p056606' => 'qlo', 'QL08p056627' => 'qlo', 'RcHm_v2.0_Chr1g0363931' => 'rch', 'RcHm_v2.0_Chr5g0060041' => 'rch', 'RcHm_v2.0_Chr5g0060321' => 'rch', 'Rhsim01G0195800' => 'rsi', 'Rhsim03G0123700' => 'rsi', 'Rhsim08G0043300' => 'rsi', 'Rhsim13G0093100' => 'rsi', 'Rhsim13G0202200' => 'rsi', 'Sabra08G0029100' => 'sbr', 'Sabra09G0009300' => 'sbr', 'Sabra09G0009500' => 'sbr', 'SalBow3G2093' => 'sbo', 'SalBow3G3621' => 'sbo', 'SalBow3G4476' => 'sbo', 'Sc15g0002250' => 'sci', 'Sc15g0002280' => 'sci', 'Sc20g0002000' => 'sci', 'Sed0015595' => 'sed', 'Sed0027444' => 'sed', 'Sed0027820' => 'sed', 'SEGI_01181' => 'sgi', 'SEGI_06073' => 'sgi', 'SEGI_08896' => 'sgi', 'SEGI_17794' => 'sgi', 'SEGI_19017' => 'sgi', 'SEGI_26462' => 'sgi', 'SEGI_37451' => 'sgi', 'SGA_v2.0_scaffold61G21163' => 'sas', 'SGA_v2.0_scaffold97G29190' => 'sas', 'SGA_v2.0_scaffold97G29192' => 'sas', 'SHI06073' => 'shi', 'SHI06074' => 'shi', 'SHI06077' => 'shi', 'SHI06079' => 'shi', 'SMO115G0269' => 'smo', 'SMO203G0240' => 'smo', 'SMO348G0031' => 'smo', 'SMO367G1086' => 'smo', 'Solyc06g010000.3' => 'sly', 'Solyc06g010100.2' => 'sly', 'Solyc06g073560.4' => 'sly', 'Solyc11g069160.3' => 'sly', 'Solyc11g069180.2' => 'sly', 'Sopen06g004740' => 'spe', 'Sopen06g029920' => 'spe', 'Sopen11g027900' => 'spe', 'Sopen11g027920' => 'spe', 'Sp5g16000' => 'spa', 'Sp5g16010' => 'spa', 'Sp6g22000' => 'spa', 'TAR369G0129' => 'tar', 'TAR633G2599' => 'tar', 'TAR633G2611' => 'tar', 'TAR636G1502' => 'tar', 'THA.LOC104799491' => 'tha', 'THA.LOC104810846' => 'tha', 'THA.LOC104814835' => 'tha', 'Thecc.09G258900' => 'tca', 'Thecc.09G259200' => 'tca', 'Thecc.10G069900' => 'tca', 'Thhalv10002397m.g' => 'esa', 'Thhalv10002530m.g' => 'esa', 'Thhalv10012623m.g' => 'esa', 'TPR.G15537' => 'tpr', 'TPR.G15539' => 'tpr', 'TPR.G27029' => 'tpr', 'TWI31G0844' => 'twi', 'TWI75G0049' => 'twi', 'TWI75G1876' => 'twi', 'TWI79G0408' => 'twi', 'unitig_46.g18231' => 'ugi', 'unitig_747.g22005' => 'ugi', 'unitig_747.g22006' => 'ugi', 'vmacro03181' => 'vma', 'vmacro04097' => 'vma', 'vmacro07086' => 'vma', 'vmacro14283' => 'vma', 'VMungo1080G0608' => 'vmu', 'VMungo1081G0001' => 'vmu', 'VMungo1127G0481' => 'vmu', 'VMungo1127G1219' => 'vmu', 'VMungo1272G0001' => 'vmu', 'Zm00001eb163160' => 'zma', 'Zm00001eb265270' => 'zma', 'Zm00001eb265410' => 'zma', 'Zm00001eb355050' => 'zma', 'Zm00001eb355110' => 'zma' ) $gf_id = 'HOM05D001528' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001528' ) $data_identifier = 'HOM05D001528' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 3, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 7, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355110' $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